
Extract Intan Data
--------------------
Creating empty HDF5 store with raw data groups
Writing RN20_4taste_preCTA.h5 ...Done!

Creating empty arrays in hdf5 store for raw data...Done!
Extracting Intan data to HDF5 Store:
 h5 file: /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA.h5

Reading time data...
Writing time data...Done!

----------
Extracting Digital Signal Data
----------
Reading digitalin data from board-DIN-00.dat...Done!
Writing data from ditigal in channel 0 to dig_in_0...Done!
Reading digitalin data from board-DIN-01.dat...Done!
Writing data from ditigal in channel 1 to dig_in_1...Done!
Reading digitalin data from board-DIN-02.dat...Done!
Writing data from ditigal in channel 2 to dig_in_2...Done!
Reading digitalin data from board-DIN-03.dat...Done!
Writing data from ditigal in channel 3 to dig_in_3...Done!
Done! Elapsed Time: 4.71


----------
Extracting Amplifier Signal Data
----------
Reading data from amp-C-000.dat...Done!
Writing data from port C channel 0 to electrode0...Done!
Reading data from amp-C-001.dat...Done!
Writing data from port C channel 1 to electrode1...Done!
Reading data from amp-C-002.dat...Done!
Writing data from port C channel 2 to electrode2...Done!
Reading data from amp-C-003.dat...Done!
Writing data from port C channel 3 to electrode3...Done!
Reading data from amp-C-004.dat...Done!
Writing data from port C channel 4 to electrode4...Done!
Reading data from amp-C-005.dat...Done!
Writing data from port C channel 5 to electrode5...Done!
Reading data from amp-C-006.dat...Done!
Writing data from port C channel 6 to electrode6...Done!
Reading data from amp-C-007.dat...Done!
Writing data from port C channel 7 to electrode7...Done!
Reading data from amp-C-008.dat...Done!
Writing data from port C channel 8 to electrode8...Done!
Reading data from amp-C-009.dat...Done!
Writing data from port C channel 9 to electrode9...Done!
Reading data from amp-C-010.dat...Done!
Writing data from port C channel 10 to electrode10...Done!
Reading data from amp-C-011.dat...Done!
Writing data from port C channel 11 to electrode11...Done!
Reading data from amp-C-012.dat...Done!
Writing data from port C channel 12 to electrode12...Done!
Reading data from amp-C-013.dat...Done!
Writing data from port C channel 13 to electrode13...Done!
Reading data from amp-C-014.dat...Done!
Writing data from port C channel 14 to electrode14...Done!
Reading data from amp-C-015.dat...Done!
Writing data from port C channel 15 to electrode15...Done!
Reading data from amp-C-016.dat...Done!
Writing data from port C channel 16 to electrode16...Done!
Reading data from amp-C-017.dat...Done!
Writing data from port C channel 17 to electrode17...Done!
Reading data from amp-C-018.dat...Done!
Writing data from port C channel 18 to electrode18...Done!
Reading data from amp-C-019.dat...Done!
Writing data from port C channel 19 to electrode19...Done!
Reading data from amp-C-020.dat...Done!
Writing data from port C channel 20 to electrode20...Done!
Reading data from amp-C-021.dat...Done!
Writing data from port C channel 21 to electrode21...Done!
Reading data from amp-C-022.dat...Done!
Writing data from port C channel 22 to electrode22...Done!
Reading data from amp-C-023.dat...Done!
Writing data from port C channel 23 to electrode23...Done!
Reading data from amp-C-024.dat...Done!
Writing data from port C channel 24 to electrode24...Done!
Reading data from amp-C-025.dat...Done!
Writing data from port C channel 25 to electrode25...Done!
Reading data from amp-C-026.dat...Done!
Writing data from port C channel 26 to electrode26...Done!
Reading data from amp-C-027.dat...Done!
Writing data from port C channel 27 to electrode27...Done!
Reading data from amp-C-028.dat...Done!
Writing data from port C channel 28 to electrode28...Done!
Reading data from amp-C-029.dat...Done!
Writing data from port C channel 29 to electrode29...Done!
Reading data from amp-C-030.dat...Done!
Writing data from port C channel 30 to electrode30...Done!
Reading data from amp-C-031.dat...Done!
Writing data from port C channel 31 to electrode31...Done!
Done! Elapsed Time: 60.48

Writing electrode_map to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA.h5...
Writing digital_input_map to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA.h5...
Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p


Data Extraction Complete
--------------------

----------
Gathering Trial Data and Creating Table
----------
Generating trial list for digital inputs: 0, 1, 2, 3
Grabbing data for digital input 0...Done!
Grabbing data for digital input 1...Done!
Grabbing data for digital input 2...Done!
Grabbing data for digital input 3...Done!
Constructing DataFrame...Done!
Writing data to h5 file...Done!
Done! Elapsed Time: 2.67

No digital output data found
Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p

CAR Groups

Group 0	Group 1
-------	-------
0	8
1	9
2	10
3	11
4	12
5	13
6	14
7	15
24	16
25	17
26	18
27	19
28	20
29	21
30	22
31	23

----------
Common Average Referencing
----------
Common Average Referencing Electrodes:
0, 1, 2, 3, 4, 5, 6, 7, 24, 26, 27, 28, 29, 30, 31
Computing common average...Done!
Storing common average signal...Done!
Storing referenced signals...Done!
Done! Elapsed Time: 49.68


----------
Common Average Referencing
----------
Common Average Referencing Electrodes:
8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23
Computing common average...Done!
Storing common average signal...Done!
Storing referenced signals...Done!
Done! Elapsed Time: 51.62


----------
Compressing and repacking h5 file
----------
Repacking /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA.h5 as /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/tmp.h5...
Removing old h5 file: /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA.h5
Renaming temporary file to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA.h5
Done! Elapsed Time: 213.45

Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p


Running Spike Detection
-------------------
Parameters
file_dir             /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745
data_quality         clean
sampling_rate        30000.0
clustering_params    
    Max Number of Clusters      7
    Max Number of Iterations    1000
    Convergence Criterion       0.001
    GMM random restarts         10
    
data_params          
    V_cutoff for disconnected headstage     1500
    Max rate of cutoff breach per second    0.2
    Max allowed seconds with a breach       10
    Max allowed breaches per second         20
    Intra-cluster waveform amp SD cutoff    3
    
bandpass_params      
    Lower freq cutoff    300
    Upper freq cutoff    3000
    
spike_snapshot       
    Time before spike (ms)    0.5
    Time after spike (ms)     1
    

Electrode    Result    Cutoff (s)
  0            1         2022
  1            1         2022
  2            1         2022
  3            1         2022
  4            1         2022
  5            1         2022
  6            1         2022
  7            1         2022
  8            1         2022
  9            1         2022
  10           1         2022
  11           1         2022
  12           1         2022
  13           1         2022
  15           1         2022
  16           1         2022
  17           1         2022
  18           1         2022
  19           1         2022
  20           1         2022
  21           1         2022
  22           1         2022
  23           1         2022
  24           1         2022
  26           1         2022
  27           1         2022
  28           1         2022
  29           1         2022
  30           1         2022
  31           1         2022
1 - Sucess
0 - No data or no spikes
-1 - Error
Writing electrode_map to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA.h5...
Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p

Spike Detection Complete
------------------

----------
Clustering Cleanup
----------
Removing raw data from hdf5 store...Done!
Removing referenced data from hdf5 store...Done!

----------
Compressing and repacking h5 file
----------
Repacking /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA.h5 as /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/tmp.h5...
Removing old h5 file: /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA.h5
Renaming temporary file to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA.h5
Done! Elapsed Time: 16.84

Done! Elapsed Time: 23.68

Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p


Running Blech Clust
-------------------
Parameters
file_dir             /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745
data_quality         clean
sampling_rate        30000.0
clustering_params    
    Max Number of Clusters      11
    Max Number of Iterations    1000
    Convergence Criterion       0.001
    GMM random restarts         10
    
data_params          
    V_cutoff for disconnected headstage     1500
    Max rate of cutoff breach per second    0.2
    Max allowed seconds with a breach       10
    Max allowed breaches per second         20
    Intra-cluster waveform amp SD cutoff    3
    
bandpass_params      
    Lower freq cutoff    300
    Upper freq cutoff    3000
    
spike_snapshot       
    Time before spike (ms)    0.5
    Time after spike (ms)     1
    

Writing electrode_map to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA.h5...
Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p

Clustering Complete
------------------

----------
Clustering Cleanup
----------
Done! Elapsed Time: 0.05

Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p


Running Blech Clust
-------------------
Parameters
file_dir                  /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745
data_quality              clean
sampling_rate             30000.0
clustering_params         
    Max Number of Clusters      11
    Max Number of Iterations    1000
    Convergence Criterion       0.001
    GMM random restarts         10
    
data_params               
    V_cutoff for disconnected headstage     1500
    Max rate of cutoff breach per second    0.2
    Max allowed seconds with a breach       10
    Max allowed breaches per second         20
    Intra-cluster waveform amp SD cutoff    3
    
bandpass_params           
    Lower freq cutoff    300
    Upper freq cutoff    3000
    
spike_snapshot            
    Time before spike (ms)    0.5
    Time after spike (ms)     1
    
max_clusters              11
max_iterations            1000
threshold                 0.001
num_restarts              10
wf_amplitude_sd_cutoff    3

Writing electrode_map to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA.h5...
Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p

Clustering Complete
------------------

----------
Deleting unit 0 from dataset
----------

Renaming following units...
Finished deleting unit
----------
Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p


----------
Clustering Cleanup
----------
Done! Elapsed Time: 0.00

Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p


---------
Beginning unit similarity calculation
----------
Computing similarity between Unit 0 and Unit 0
Computing similarity between Unit 0 and Unit 1
Computing similarity between Unit 0 and Unit 2
Computing similarity between Unit 0 and Unit 3
Computing similarity between Unit 0 and Unit 4
Computing similarity between Unit 0 and Unit 5
Computing similarity between Unit 1 and Unit 0
Computing similarity between Unit 1 and Unit 1
Computing similarity between Unit 1 and Unit 2
Computing similarity between Unit 1 and Unit 3
Computing similarity between Unit 1 and Unit 4
Computing similarity between Unit 1 and Unit 5
Computing similarity between Unit 2 and Unit 0
Computing similarity between Unit 2 and Unit 1
Computing similarity between Unit 2 and Unit 2
Computing similarity between Unit 2 and Unit 3
Computing similarity between Unit 2 and Unit 4
Computing similarity between Unit 2 and Unit 5
Computing similarity between Unit 3 and Unit 0
Computing similarity between Unit 3 and Unit 1
Computing similarity between Unit 3 and Unit 2
Computing similarity between Unit 3 and Unit 3
Computing similarity between Unit 3 and Unit 4
Computing similarity between Unit 3 and Unit 5
Computing similarity between Unit 4 and Unit 0
Computing similarity between Unit 4 and Unit 1
Computing similarity between Unit 4 and Unit 2
Computing similarity between Unit 4 and Unit 3
Computing similarity between Unit 4 and Unit 4
Computing similarity between Unit 4 and Unit 5
Computing similarity between Unit 5 and Unit 0
Computing similarity between Unit 5 and Unit 1
Computing similarity between Unit 5 and Unit 2
Computing similarity between Unit 5 and Unit 3
Computing similarity between Unit 5 and Unit 4
Computing similarity between Unit 5 and Unit 5

Similarity calculation done!
No unit similarity violations found!
Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p

Generating unit arrays with parameters:
----------
    dig_ins_to_use    
            0,     1,     2,     3
    laser_channels    
        
    sampling_rate     30000.0
    pre_stimulus      2000
    post_stimulus     5000
    

----------
Making Unit Spike Arrays
----------


----------
Reading Trial Data Table From Store
----------
Done! Elapsed Time: 0.03


----------
Reading Trial Data Table From Store
----------
Done! Elapsed Time: 0.01

Creating spike arrays for dig_in_0...
Creating spike arrays for dig_in_1...
Creating spike arrays for dig_in_2...
Creating spike arrays for dig_in_3...
Done with spike array creation!
----------

Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p

Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p


----------
Deleting unit 2 from dataset
----------

Renaming following units...
Renaming unit003 to unit002
Renaming unit004 to unit003
Renaming unit005 to unit004
Correcting names of plots and metrics...
Finished deleting unit
----------
Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p


---------
Beginning unit similarity calculation
----------
Computing similarity between Unit 0 and Unit 0
Computing similarity between Unit 0 and Unit 1
Computing similarity between Unit 0 and Unit 2
Computing similarity between Unit 0 and Unit 3
Computing similarity between Unit 0 and Unit 4
Computing similarity between Unit 0 and Unit 5
Computing similarity between Unit 1 and Unit 0
Computing similarity between Unit 1 and Unit 1
Computing similarity between Unit 1 and Unit 2
Computing similarity between Unit 1 and Unit 3
Computing similarity between Unit 1 and Unit 4
Computing similarity between Unit 1 and Unit 5
Computing similarity between Unit 2 and Unit 0
Computing similarity between Unit 2 and Unit 1
Computing similarity between Unit 2 and Unit 2
Computing similarity between Unit 2 and Unit 3
Computing similarity between Unit 2 and Unit 4
Computing similarity between Unit 2 and Unit 5
Computing similarity between Unit 3 and Unit 0
Computing similarity between Unit 3 and Unit 1
Computing similarity between Unit 3 and Unit 2
Computing similarity between Unit 3 and Unit 3
Computing similarity between Unit 3 and Unit 4
Computing similarity between Unit 3 and Unit 5
Computing similarity between Unit 4 and Unit 0
Computing similarity between Unit 4 and Unit 1
Computing similarity between Unit 4 and Unit 2
Computing similarity between Unit 4 and Unit 3
Computing similarity between Unit 4 and Unit 4
Computing similarity between Unit 4 and Unit 5
Computing similarity between Unit 5 and Unit 0
Computing similarity between Unit 5 and Unit 1
Computing similarity between Unit 5 and Unit 2
Computing similarity between Unit 5 and Unit 3
Computing similarity between Unit 5 and Unit 4
Computing similarity between Unit 5 and Unit 5

Similarity calculation done!
No unit similarity violations found!
Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p

Generating unit arrays with parameters:
----------
    dig_ins_to_use    
            0,     1,     2,     3
    laser_channels    
        
    sampling_rate     30000.0
    pre_stimulus      2000
    post_stimulus     5000
    

----------
Making Unit Spike Arrays
----------


----------
Reading Trial Data Table From Store
----------
Done! Elapsed Time: 0.01


----------
Reading Trial Data Table From Store
----------
Done! Elapsed Time: 0.01

Creating spike arrays for dig_in_0...
Creating spike arrays for dig_in_1...
Creating spike arrays for dig_in_2...
Creating spike arrays for dig_in_3...
Done with spike array creation!
----------

Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p

Saved RN20_4taste_preCTA to /data/Katz_Data/Stk11_Project/RN20/RN20_4taste_preCTA_191016_123745/RN20_4taste_preCTA_dataset.p

